SHORE, for Short Read, is a mapping and analysis pipeline for short read data produced on the Illumina platform. It allows the incorporation of different aligners, and its different modules support a range of experiments, such as resequencing, mapping of mutants, ChIP-seq analyses and several more.

Downloads

SHORE is now hosted on sourceforge. You can access the source code via git:

$ git clone https://git.code.sf.net/p/shore/code shore-code

Documentation:

http://shore.sourceforge.net/wiki/

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